8SEA: Ubiquitin-like modifier-activating enzyme 7

Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex (Form 1). Determined by electron microscopy at 3.4 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,208
Mol. weight: 164.11 kDa
Ligands: AMP
Released: 11 Oct 2023

Explore 8SEA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SEA contains 75 α-helices and 69 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 63 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	24-31	8
β-strand	34-38	5	1
α-helix	42-54	13
β-strand	58-62	5	1
β-strand	66	1	2
α-helix	67	1
α-helix	70-73	4
β-strand	86	1	2
α-helix	87-98	12
β-strand	103-106	4	1
α-helix	110-111	2
α-helix	113-118	6
β-strand	121-124	4	1
α-helix	129-141	13
β-strand	145-147	3	1
β-strand	150-152	3	3
β-strand	153	1	4
β-strand	155-159	5	3
β-strand	160-161	2	1
β-strand	166-168	3	5
β-strand	170	1	6
α-helix	175-177	3
β-strand	178-179	2	7
β-strand	181-184	4	8
β-strand	191-194	4	8
α-helix	198-202	5
β-strand	208-210	3	7
β-strand	214-216	3	9
α-helix	218-220	3
β-strand	226-227	2	7
β-strand	231	1	10
β-strand	235	1	10
β-strand	236-237	2	8
β-strand	247-250	4	9
β-strand	253-256	4	7
α-helix	257-259	3
β-strand	260-262	3	5
α-helix	267-272	6
α-helix	281-304	24
α-helix	307-309	3
α-helix	313-325	13
α-helix	328-330	3
α-helix	340-342	3
α-helix	343-351	9
β-strand	356	1	4
α-helix	358-377	20
β-strand	379	1	6
β-strand	386-390	5	3
α-helix	392-394	3
α-helix	396-397	2
α-helix	401-404	4
α-helix	405-408	4
α-helix	416-422	7
α-helix	424-432	9
β-strand	437-438	2	11
α-helix	443-454	12
β-strand	466-467	2	11
β-strand	471	1	12
α-helix	474-477	4
α-helix	485-487	3
β-strand	491	1	12
α-helix	492-503	12
β-strand	511-512	2	11
α-helix	518-520	3
α-helix	526-531	6
β-strand	535-537	3	11
α-helix	542-555	14
β-strand	559-563	5	11
β-strand	568-574	7	11
α-helix	580-582	3
α-helix	586-592	7
α-helix	595-597	3
α-helix	599-602	4
α-helix	608-630	23
α-helix	632-636	5
α-helix	645-650	6
α-helix	654-656	3
α-helix	673-677	5
α-helix	678-682	5
α-helix	683-691	9
α-helix	722-739	18
α-helix	743-745	3
α-helix	750-756	7
α-helix	762-764	3
α-helix	783-799	17
α-helix	801-805	5
α-helix	818-831	14
α-helix	834-837	4
α-helix	839-844	6
α-helix	849-853	5
α-helix	854-872	19
α-helix	878-880	3
β-strand	883-887	5	11
β-strand	892-896	5	11
α-helix	897-902	6
β-strand	904-906	3	13
β-strand	909-911	3	13
β-strand	917-919	3	14
α-helix	925-926	2
β-strand	927	1	15
α-helix	928-939	12
β-strand	945-948	4	16
β-strand	951-955	5	16
α-helix	960-966	7
β-strand	970	1	15
α-helix	971-979	9
α-helix	982-984	3
β-strand	989-992	4	14
β-strand	993-994	2	16
α-helix	1005-1007	3
β-strand	1008-1011	4	14

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	80-81	2
β-strand	82-87	6	17
β-strand	93-98	6	17
β-strand	103	1	18
α-helix	104-115	12
β-strand	122-126	5	17
β-strand	129-130	2	17
β-strand	136	1	18
β-strand	147-152	6	17
α-helix	153-154	2

Chain C: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-16	14
β-strand	22-26	5	19
β-strand	34-39	6	19
α-helix	46-48	3
β-strand	49-50	2	20
β-strand	51-56	6	19
β-strand	67-70	4	19
β-strand	76	1	21
β-strand	79	1	21
β-strand	84	1	19
β-strand	85	1	21
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15
β-strand	149-150	2	20
α-helix	151-152	2

Chain D: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	86	1	22
α-helix	104-115	12
α-helix	119-121	3
β-strand	124-126	3	22
β-strand	129	1	22
α-helix	137-140	4
β-strand	148-150	3	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 7	A	protein	1012	Homo sapiens	P41226 (AlphaFold model)
Ubiquitin-like protein ISG15	B, D	protein	157	Homo sapiens	P05161 (AlphaFold model)
Ubiquitin/ISG15-conjugating enzyme E2 L6	C	protein	152	Homo sapiens	O14933 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8SEA_1 Ubiquitin-like modifier-activating enzyme 7 (chains A)
MDALDASKLLDEELYSRQLYVLGSPAMQRIQGARVLVSGLQGLGAEVAKNLVLMGVGSLT
LHDPHPTCWSDLAAQFLLSEQDLERSRAEASQELLAQLNRAVQVVVHTGDITEDLLLDFQ
VVVLTAAKLEEQLKVGTLCHKHGVCFLAADTRGLVGQLFCDFGEDFTVQDPTEAEPLTAA
IQHISQGSPGILTLRKGANTHYFRDGDLVTFSGIEGMVELNDCDPRSIHVREDGSLEIGD
TTTFSRYLRGGAITEVKRPKTVRHKSLDTALLQPHVVAQSSQEVHHAHCLHQAFCALHKF
QHLHGRPPQPWDPVDAETVVGLARDLEPLKRTEEEPLEEPLDEALVRTVALSSAGVLSPM
VAMLGAVAAQEVLKAISRKFMPLDQWLYFDALDCLPEDGELLPSPEDCALRGSRYDGQIA
VFGAGFQEKLRRQHYLLVGAGAIGCELLKVFALVGLGAGNSGGLTVVDMDHIERSNLSRQ
FLFRSQDVGRPKAEVAAAAARGLNPDLQVIPLTYPLDPTTEHIYGDNFFSRVDGVAAALD
SFQARRYVAARCTHYLKPLLEAGTSGTWGSATVFMPHVTEAYRAPASAAASEDAPYPVCT
VRYFPSTAEHTLQWARHEFEELFRLSAETINHHQQAHTSLADMDEPQTLTLLKPVLGVLR
VRPQNWQDCVAWALGHWKLCFHYGIKQLLRHFPPNKVLEDGTPFWSGPKQCPQPLEFDTN
QDTHLLYVLAAANLYAQMHGLPGSQDWTALRELLKLLPQPDPQQMAPIFASNLELASASA
EFGPEQQKELNKALEVWSVGPPLKPLMFEKDDDSNFHVDFVVAAASLRCQNYGIPPVNRA
QSKRIVGQIIPAIATTTAAVAGLLGLELYKVVSGPRPRSAFRHSYLHLAENYLIRYMPFA
PAIQTFHHLKWTSWDRLKVPAGQPERTLESLLAHLQEQHGLRVRILLHGSALLYAAGWSP
EKQAQHLPLRVTELVQQLTGQAPAPGQRVLVLELSCEGDDEDTAFPPLHYEL

Sequence of entity 2 (B, D), FASTA

>8SEA_2 Ubiquitin-like protein ISG15 (chains B, D)
MGWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPL
ASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDD
LFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGG

Sequence of entity 3 (C), FASTA

>8SEA_3 Ubiquitin/ISG15-conjugating enzyme E2 L6 (chains C)
MASMRVVKELEDLQKKPPPYLRNLSSDDANVLVWHALLLPDQPPYHLKAFNLRISFPPEY
PFKPPMIKFTTKIYHPNVDENGQICLPIISSENWKPSTKTSQVLEALNVLVNRPNIREPK
RMDLADLLTQNPELFRKNAEEFTLRFGVDRPS

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	1

Primary citation

Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer. Afsar, M., Liu, G., Jia, L. et al. Nat Commun (2023) 14:4786-4786. DOI 10.1038/s41467-023-39780-z · PubMed

Other PDB entries of the same protein (UniProt P41226 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SE9 3.2 Å, Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex…
8SEB 3.24 Å, Cryo-EM structure of a single loaded human UBA7-UBE2L6-ISG15 adenylate complex
8SV8 3.38 Å, Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex…
8OIF 3.5 Å, Structure of the UBE1L activating enzyme bound to ISG15 and UBE2L6
8WWX Ube1L acts akin to a mitt, that mediates UbcH8 binding and orchestrates "E1-E2"…

Browse structure collections

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